Genome-Wide Characterization, Expression Profiling and Source-Sink Nitrogen Responses of Rice Glutamine Synthetase Gene Family

Background: Nitrogen is the most abundant mineral nutrient required by rice (Oryza sativa) and the primary limiting factor for grain yield. Glutamine synthetase (GS) is a key enzyme involved in nitrogen assimilation in rice, and is closely associated with nitrogen use efficiency (NUE) and source–sink nitrogen dynamics. Methods: We performed a genome-wide characterization of the GS gene family across 12 plant species. Haplotype analysis of four rice GS genes was conducted using resequencing data from approximately 2000 rice accessions. A reproductive-stage nitrogen-gradient experimental system (0N, 1N, 3N) was established to simultaneously profile GS transcript levels and enzyme activity in source tissues (roots and flag leaves) and sink tissues (young embryos at different developing stages). Results: A total of 86 non-redundant GS proteins were identified, which clustered into two evolutionarily distinct subfamilies (GS1 and GS2). In rice, OsGS1-1 exhibited pronounced indica–japonica differentiation and a pattern consistent with a domestication bottleneck, while other members showed high sequence conservation. Transcript abundance and enzymatic activity data revealed that OsGS1‑3 among GS isoforms exhibited its highest transcript level at 5 days after pollination (DAP), while total GS activity peaked at 5 DAP in developing embryos, suggesting this stage may represent a critical window for active nitrogen assimilation during embryogenesis. Distinct tissue-specific expression patterns and nitrogen-responsive profiles were also observed among OsGS isoforms. Conclusions: These findings provide fundamental insights into the evolutionary and functional diversification of the rice GS gene family. The tissue-specific and nitrogen-dependent transcriptional and enzymatic responses of GS isoforms indicate their coordinated involvement in nitrogen assimilation processes, which may further influence source–sink nitrogen utilization in rice under varying nitrogen conditions.